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Contact Info

SKILLS

Experience

Languages

Polish: Native

English: Proficient (C1)

Main

Wiesław Abramowicz, M.S.

Oncological Molecular Biologist & Computational Scientist

using proteasomes inhibitor, nutritranscriptomics

Research Experience

Transcriptomic profiling of a human kidney cancer cell line, Caki-2, after treatment of Ixazomib, Ursolic acid and jointly using microarray technology.

Advisor: Prof. Marzanna Cechowska-Pasko, Ph.D.

Department of Pharmaceutical Biochemistry, Medical University of Białystok.

  • Budget management (successful negotiations with vendors within budget);
  • Project manager and executive (wet lab, in silico analyses);
  • Performed wet laboratory experiments (Agilent’s gene expression and miRNA microarrays of indirect transcriptome form total RNA (mRNA, lncRNA, lincRNA, sno/snRNA, ncRNA, miscRNA, miRNA), quality controls (pos/neg/spike-in), MTT drug testing (proteasome inhibitor, terpen), total RNA/DNA isolation, purification, quality, quantity (Bioanalyzer, NanoDrop), gene validation (qPCR, primer design, analysis))
  • and in silico using open-source programming/biostatistical R/RStudio with packages from cran, bioconductor, github repos (pre-processing, numerical validation awarness, glm, Bayesian, multivariate, pathway enrichment analysis). On time delivering wet lab experiments (I take care of the details and I am very precise, successful troubleshooting), performing and precaution of misleading computational analysis. [manuscript in preparation]

8/2017 - 10/2013

DNA sequencing of clear cell renal cell carcinoma and healthy kidney area (clinical cases).

“Genome-wide methods in cancer genetics”. BASTION. Advisor: Prof. Marzanna Cechowska-Pasko, Ph.D.

Department of Pharmaceutical Biochemistry, Medical University of Białystok.

  • project co-executive (wet lab, in silico analyses);
  • DNA sequencing (1000 genes) of human cancer and normal kidney using KAPA library. [with co-operation of Prof. Rafał Płoski, MD, PhD (Medical University of Warsaw). [manuscript in preparation]

12/2015 - 10/2014

Driving licence

AM/B1/B

Smooth driving, dynamic driving, no collisions.

N/A

Currently - 30/08/2006

In Silico

Biostatistic experience

Interests: pre-processing (raw signal, transformations), manifolds/topology, glm, gee, mixed models

N/A

N/A

  • exploratory and confirmatory analyses;
  • GLMs & Bayesian, mixed (limma, mmrm, lme4);
  • R, RStudio;
  • R packages (GO.db, pathview, RSubread, Gviz, biomaRt, plotly, ggplot, etc.);
  • R programming (visualizations, office documentation, pdf, rtf);
  • data mining, regular expression, rest api;
  • pre-processing (log, lowess, loess, quantile) of transcriptomics data;
  • Reproducible tools (git, github, gitlab) and reporting (rmarkdown, bookdown, etc.);
  • Pathway Enrichment Analysis (GO, KEGG, Reactome, WikiPathways, HumanCyc, clusterProfiler, rSEA);
  • Multivariate Analysis (PCA, tSNE, UMAP, SONG, NMF, Ricci flow);
  • Comparative Analysis (Venn diagram);
  • Isobolograms;
  • use of data sets (ncbi, google patents, etc.);
  • use of FDA resources (CDER, CDRH, NCTR – mitochondial toxicity, MAQC/SEQC);
  • numerical validation awarness;
  • Linux command line;
  • basics of MySQL;
  • basics of Python (PyScripter, PyMol, PyLasso, Autodock/Vina);
  • basics of machine Learning (Random forest, CatBoost, LightGBM, XGBoost, H2O);
  • basics of neural Networks (TensorFlow, Keras, etc.);
  • Agilent’s GeneSpring GX;
  • CLC Main Workbench;
  • more information in each description of course;

HPC experience

High-Performance and Parallel Computing

N/A

N/A

  • I built cluster of two personal computers with openMPI and Rmpi (an interface for R & RStudio) on Ubuntu (SSH connected).

Wet Lab

Laboratory Experience

Research interests: Oncology, Immunology, EpiOmics, Transcriptomic, Proteasomes, Nutritranscriptomics, Watson-Crick/Hoogsteen base paring.

Medical University of Białystok, PL

2017 - 2011

  • BIO-RAD CFX Connect Real-Time PCR (qPCR);
  • Agilent’s microarray (two-color gene expression, miRNA) + QC (positive, negative, spike-in controls);
  • NanoDrop 2000 (spectrophotometry);
  • MTT tests (using proteasome inhibitor {Ixazomib} – on-label FDA approved in multiple myeloma, terpen {Ursolic acid} – derivative, from e.g. apples, with anti-inflammation, anti-cancer properties);
  • DNA, RNA extraction from cultured cells (Qiagen, Promega, A&A Biotechnology); RNase, DNase free environment;
  • Agilent 2100 Bioanalyzer (DNA/RNA microcapillary electrophoresis, flow cytometry) – lab-on-chip;
  • DNA, RNA gel electrophoresis;
  • Western blot with SNAP i.d.;
  • PMN, PBMC cells isolation, neutrophils isolation with anti-CD16 mAb MicroBeads and magnetic separator Midi MACS;
  • cells counting chambers;
  • setting up cell cultures;
  • optical microscope;
  • flow cytometry.

Education

Ph.D. Studies in Pharmaceutical Sciences (resign)

The Center for Innovative Research 2012-2017, Faculty of Medicine with the Division of Dentistry and Division of Medical Education in English, Faculty of Pharmacy and Division of Laboratory Medicine, Medical University of Białystok

PL

08/2017 - 10/2013

Research area: Transcriptomic profiling of cancer cell line after drugs treatment using Agilent microarrays and biostatistic open-source tools.

Advisor: Prof. dr hab. Marzanna Cechowska-Pasko, Ph.D.

All subjects passed (GPA 3,85):

  • Principles of genetic analysis (6h);
  • Learning techniques of molecular biology (10h);
  • Introduction to genomics (6h);
  • Epigenomics and transcriptomics (50h);
  • Learning methods in structural and functional genomics (10h);
  • Basic Statistical refreshment (30h; prof. Tomasz Burzykowski, UHasselt);
  • Statistical modeling (30h; prof. Tomasz Burzykowski, UHasselt);
  • Design of experiments (18h; prof. Tomasz Burzykowski, UHasselt);
  • Statistics for omics (36h; prof. Ziv Shkedy, UHasselt);
  • Metabolomics (16h);
  • Facultative advanced courses in protein analysis/ proteomics/ metabolomics (50h);
  • Protein analysis and proteomics (32h);
  • Immunology (16h);
  • Facultative advanced courses in immunology (15h);
  • Teaching the presentation and evaluation of research at the academic level (30h);
  • Professional practice (30h);
  • OHS (4h).

M.Sc. in Medical Analitics, PQF 7

Faculty of Pharmacy and Division of Laboratory Medicine, Medical University of Białystok

PL

09/2013 - 10/2007

Master’s thesis: Expression of the APRIL particle in neutrophils of patients with potentially malignant lesions of the oral mucosa.

  • GPA: 4,30 (transcript of master degree);
  • isolation and work with human blood cells;
  • Advisor: Prof. dr hab. Ewa Jabłońska, Ph.D.
  • Co-Advisor: dr Kamil Grubczak, Ph.D.
  • experience in biochemistry and immunology research (see Wet lab, Student membership & Publications sections in this resume);
  • Dean’s leave (10/2008 - 09/2009)

Pharmaceutical Assistant, PQF 4

Vocational School No. 1 of Health Care

Białystok, PL

08/2007 - 09/2005

Employment

Owner, Co-founder & CEO

WARZEM Wood & Stone, Solid Wood Artistic Carpentry Workshop.

Dąbrowa Białostocka, PL

12/2022 - 4/2021

● management, accountancy; ● website design and build with html5, css, js, yaml, github;
● graphic design and creation (Inkscape – vector graphics); ● creating solid wood furnitures (using the golden ratio); ● carpentry tools design and create; ● using natural oils (no siccative, no PFAS) – toxicological issues; ● chopping down trees;

Pharmaceutical Assistant

Pharmacy “Lobelia” Barbara Winsko.

Białystok, PL

09/2009 - 09/2008

● advising for patients in OTC medication; ● issuing medicines prescribed by a physician; ● accepting and placing orders; ● delivering medicines to other points of sale.

Professional membership

The Right to Practice the Profession in Laboratory Diagnostic. No 13786

KIDL

Warsaw

12/2018 - 01/2014

Data Science, Laboratory Courses

Duke Industry Statistics Symposium 2023

“Empower Clinical Development by Harnessing Data from Diverse Sources”

Duke University, USA

29/ - 31/03/2023

“Good Things Come in Small Packages: Purifying miRNA from Plasma, Serum and Exosomes”

Michelle Mandrekar – Promega

Online, PL

25/01/2023

  • Maxwell RSC miRNA

Courses:

A&A Biotechnology

Gdańsk, PL

22/ - 25/09/2014

  • “Real-Time PCR”
  • “Real-Time PCR - quantitative markings”

Prof. Tomasz Motyl Laboratory Experience:

Department of Physiological Sciences, WULS (SGGW)

Warsaw, PL

10/2014

  • Agilent’s expression microarray experiments (wet lab only).

“Exploratory Data Analysis”

coursera.org – online course

Johns Hopkins University

11/2018

  • lattice.
  • ggplot2.
  • Clustering.
  • Dimension Reduction.

“NGS in Regulatory Gene Research”

ideas4biology

Poznań, PL

06/2016

Coordinator: dr Michał Szcześniak, Ph.D.

Techniques: ChIP-chip, ChIP-Seq, ChIP-exo, CLIP-Seq, DNase-Seq, FAIRE-Seq, GRO-Seq, HiC, MeDIP-Seq, MBD-Seq, MNase-Seq, oxBS-Seq, RIP-Seq, RRBS-Seq, TAB-Seq, TSS-Seq, WGBS-Seq.

Linux. WinSCP, PuTTY.

Softwares: POLYPHEMUS, ChromHMM, Segway, MACE, DANPOS2, MeDUSA, diffReps, BSMAP, methylKit, Trimmomatic, Subread, BamTools.

Databases: OMICtools, AllSeq, ChIPBase, hmChIP, mirPath, miRTarBase.

“Getting and Cleaning Data”

coursera.org – online

Johns Hopkins University

02/2016

  • dplyr, httr, rhdf5, xml, RMySQL, foreign, rmongodb, RMongo, RPostresSQL;
  • Regular Expressions.

“R programming”

coursera.org – online

Johns Hopkins University

01/2016

  • R, RStudio.

“The Data Scientist’s Toolbox”

coursera.org – online

Johns Hopkins University

01/2016

  • Version Control (Git, GitHub).
  • R Markdown.

“Using next-generation sequencing to analyse human transcriptome”

Richard Dixon, Ph.D. – QIAGEN

Medical University of Bialystok, PL

16/ - 18/06/2014

“Using next generation sequencing to analyse human genome”

Richard Dixon, Ph.D. – QIAGEN

Medical University of Bialystok, PL

08/ - 11/04/2014

“Early diagnosis and treatment of neurodegenerative diseases”

Department of Biochemical Diagnostics, Department of Neurology, Department od Neurodegeneration Diagnostics, Department of Pediatrics, Gastroenterology and Pediatric Allergology of Medical University of Bialystok

Bialystok, PL

07/04/2014

Student membership

Member of the board of the Students’ Scientific Society

Co-organizer of the 8th & 7th Białystok International Medical Congress for Young Scientists. Coordinator of Belarusian participants.

Medical University of Białystok, PL

2013 - 2012

Department of Immunology

Active participant of Student’s Scientific Society.

Medical University of Białystok, PL

06/2013 - 10/2009

Advisor: Prof. Ewa Jabłońska, Ph.D.

Department of Pharmaceutical Biochemistry

Active participant of Student’s Scientific Society.

Medical University of Białystok, PL

2011 - 2010

Advisor: dr hab. Małgorzata Borzym-Kluczyk, Ph.D.

Publications and Posters

Tylirozyd, a flavonoid with cytotoxic properties. Poster presentation.

Nationwide Scientific Symposium “Supplements a deity under the microscope of a pharmacist”.

Medical University of Bialystok, PL

2013

Abramowicz W.

APRIL molecule in patients with potentially malignant lesions of the oral mucosa (lichen planus).

7th International Medical Congress for Young Scientists, Białystok, p.185

N/A

2012

Abramowicz W., Wawrusiewicz-Kurylonek N., Garley M.

Alpha-mannosidase and beta-galactosidase activity in the serum of patients with colorectal adenocarcinoma.

5th International Scientific Conference of Medical Students and Young Doctors, Białystok, p.132-133

N/A

2010

Luto M., Choromańska B., Chwiła A., Wasiluk A., Abramowicz W.

Assessment of the activity of N-acetyl-beta-D-hexosaminidase, it’s B enzyme and betaglucuronidase in the urine of patients with Lyme disease.

5th International Scientific Conference of Medical Students and Young Doctors, Białystok, p.127

N/A

2010

Choromańska B., Luto M., Abramowicz W., Chwiła A., Wasiluk A.

The activity of N-acetyl-beta-hexosaminidase, it’s N-isoenzyme and beta-glucuronidase in the blood serum of patients suffering from Lyme disease.

5th International Scientific Conference of Medical Students and Young Doctors, Białystok, p.128

N/A

2010

Chwiła A., Luto M., Choromańska B., Wasiluk A., Abramowicz W.

Alanine and aspartic aminotransferase activity in blood serum of men after acute and chronic ethyl alcohol poisoning.

5th International Scientific Conference of Medical Students and Young Doctors, Białystok, p.137-138

N/A

2010

Wasiluk A., Abramowicz W., Luto M., Choromańska B., Chwiła A.

Hobby

Books (QCD, manifolds, new technologies, marine art), cycling in the mountains, pencil drawing, swimming, ski, interior design, DIY (wood & stone), photography.

N/A

Everywhere it is possible

Free time - 11/1986;)

Disclaimer

Last updated on 2023-05-30.